Duplicate SKUs notifications via Amazon MCF by WebBee, though there is no duplicate SKU mapped in app.
As a merchant you might have added same SKUs with more than one products/ items in Shopify.
OR could be the case where you have multiple variants under same products.
You can add the same however if you have inventory/ stock source-Amazon seller to sync back inventory to Shopify, then with same SKUs for multiple variants/ products this could be an issue and may result as inventory is never updated correctly back to Shopify.
You are recommended to have unique SKU for each variant/ each product.
This can help to sync the data-inventory, orders and tracking etc. correctly from Amazon to Shopify or visa-versa. In case you have such duplicate SKUs then just review them in Shopify and change/ edit to make them with unique name/ value, so that those are not duplicate anymore.
For more on Product Linking click here
On managing notifications including mismatch/ duplicate SKUs click here